Optical clearing & time-lapse fluorescent imaging of Live mouse Brain (up to 800 μm of depth)🤯

An acute olfactory bulb slice(P11) loaded with GCaMP6f (Ca2+ sensor) was imaged with #2PM at a depth of 150 μm during clearing with SeeDB-Live👹

#NatMethods 2026
www.nature.com/articles/s41...

SpatioTemporal Omics eneRgIES

STORIES
Learning Waddington differentiation potential (FGW loss) from #SpatialTranscriptomics (across time points) using Optimal Transport

Tunable weights of spatial information

Compute both pseudotime & velocity

#NatMethods 2025
www.nature.com/articles/s41...

#SpatialTranscriptomics

Optimizing Xenium In Situ data utility by quality assessment & best-practice analysis workflows

Must-read for Xenium user🔥

👉Segmentation
👉Spatially variable feature selection
👉Imputation
👉Spatial domain identification

#NatMethods 2025
www.nature.com/articles/s41...

Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometry - Nature Methods An ion mobility-resolved mass cytometry method for single-cell metabolomics enables multidimensional metabolomic profiling. The approach was used to curate a metabolic single-cell atlas containing 45,...

Deep-coverage single-cell metabolomics enabled by ion mobility-resolved mass cytometry #NatMethods www.nature.com/articles/s41...

Spatial Multi-omics

DBiTplus
DBiT-seq + CODEX

Mesmer segmentation
MaxFus multiomic integration
CODEX-informed spatial deconvolution (TACCO vs Cell2location vs RCTD)

Work on FFPE
>1000 genes/25 μm spot

@zongmingma.bsky.social @rongfan8.bsky.social #NatMethods 2025
www.nature.com/articles/s41...

Subcellular resolution (333 nm) Imaging Mass Cytometry🤠

Oversampling + point spread function image deconvolution

Executable on Hyperion XTi or Hyperion+ system

Resolving Nucleoli, neighboring B-T cells

25 plex Ab

#NatMethods 2025
www.nature.com/articles/s41...

#SpatialOmics

MCMICRO
Multiple Choice Microscopy pipeline
mcmicro.org

Multi-channel whole-slide images▶️
Single-cell data + Spatial Feature Tables

Multimodal (CyCIF CODEX mIHC) registration + HE IMC MIBI

#NatMethods 2022
www.nature.com/articles/s41...

Uncovering hidden protein modifications with native top-down mass spectrometry - Nature Methods precisION discovers, localizes and quantifies protein modifications within complex proteoform assemblies through data-driven analysis of native top-down mass spectra.

Uncovering hidden protein modifications with native top-down mass spectrometry #NatMethods www.nature.com/articles/s41...

MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries - Nature Methods MSnLib is a large-scale, open MSn spectral library featuring >2.3 million MSn and >357,000 MS2 spectra for 30,008 unique small molecules.

MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries #NatMethods www.nature.com/articles/s41...

Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing - Nature Methods This study introduces SDR-seq, a droplet-based single-cell DNA–RNA sequencing platform, enabling the study of gene expression profiles linked to both noncoding and coding variants.

🚨 New in Nat Methods: "Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing"

DOI: doi.org/10.1038/s415...

#Genomics #NatMethods #Transcriptomics #SDRseq #Science #SingleCell

Unified mass imaging maps the lipidome of vertebrate development - Nature Methods uMAIA is an analytical framework designed to enable the construction of metabolic atlases at high resolution using mass spectrometry imaging data.

Unified mass imaging maps the lipidome of vertebrate development #NatMethods #MassSpec www.nature.com/articles/s41...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data #NatMethods www.nature.com/articles/s41...

Empowering chemists to mine high-throughput mass spectrometry datasets - Nature Methods The Mass Query Language (MassQL) enables scientists to precisely express and reproducibly search for mass spectrometry (MS) peak patterns in large MS datasets. MassQL has been adopted across the most ...

Empowering chemists to mine high-throughput mass spectrometry datasets #NatMethods www.nature.com/articles/s41...

A universal language for finding mass spectrometry data patterns - Nature Methods The Mass Spectrometry Query Language (MassQL) is an open-source language that enables instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and ex...

A universal language for finding mass spectrometry data patterns #NatMethods www.nature.com/articles/s41...

Spatial mechano-transcriptomics👹

Image-based cell mechanics inference
Segmentation Multi-junctional molecules▶️
Circular arc polygon tiling for cell contacts▶️
Cellular pressure, junctional tension, stress tensor

+Imaging-based #SpatialTranscriptomics

#NatMethods 2025
www.nature.com/articles/s41...